
BMP CompositeFrame;
BMP BackgroundImage;
char* OutputFilename;

int Width;
int Height;
int FontSize;

double Time = 0.0;

char* created_by_string1;
char* created_by_string2;
char* copyright_string1;
char* copyright_string2;

int DiffusionLengthScaleInMicrons;
double time_scale_in_hours;

RGBApixel ViableColor;
RGBApixel HypoxicColor;
RGBApixel NecroticColor;
RGBApixel FrameColor;
RGBApixel FontColor;

RGBApixel BloodVesselColor;
RGBApixel SproutTipColor;

RGBApixel Black;
RGBApixel White;


frame TopMiddleFrame;
frame TopRightFrame;

frame LeftFrame;
frame MiddleFrame;
frame RightFrame;

frame BottomLeftFrame;
frame BottomMiddleFrame;
frame BottomRightFrame;

Matrix Phi;
Matrix PhiH;
Matrix PhiN;
Matrix X;
Matrix Y;
Matrix Structure;
Matrix MapIndicator;
Matrix Tracer;
Matrix TracerX;
Matrix TracerY;
Matrix TracerS;
Matrix TracerT;
Matrix TracerD;
Matrix Macrof;
Matrix MacrofD;
Matrix SrtX;
Matrix SrtY;
Matrix ShearRate;
Matrix MapVesselCells;
Matrix MapSproutTips;
Matrix MapFlow;
Matrix MapRadius;
Matrix MapPressure;


Matrix SproutTips;
Matrix VesselCells;
Matrix Shuffle;
Matrix VEGFR;
Matrix Notch;
Matrix Delta4;
Matrix BloodVesselIndicator;
Matrix BloodVesselRadius;
bool PlotVessels;
double min_vessel_radius;
double min_vessel_transparency;
double max_vessel_radius;
double max_vessel_transparency;

Matrix TopMiddleData;
Matrix TopRightData;

Matrix LeftData;
Matrix MiddleData;
Matrix RightData;

Matrix BottomLeftData;
Matrix BottomMiddleData;
Matrix BottomRightData;

double _EPS = 1e-16;

double BlendParameter;

char* Phi_base;
char* PhiH_base;
char* PhiN_base;
char* Structure_base;
  
char* BloodVesselRadius_base;
char* BloodVesselIndicator_base;
char* SproutTips_base;

